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Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
https://ecogenomics.github.io/GTDBTk/
GNU General Public License v3.0
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Do I need a network to run classify_wf #591

Closed zhaoxuetong closed 6 months ago

zhaoxuetong commented 6 months ago

Hi:

I might need your help. [1] On a server that cannot connect to the Internet, the following error occurs:

$ ~/.conda/envs/gtdbtk-2.3.2/bin/gtdbtk classify_wf --genome_dir /p300s/3-binning --out_dir /p300s/MAG/classify_wf --extension fa --cpus 1 --skip_ani_screen [2024-05-20 10:20:36] INFO: GTDB-Tk v2.3.2 [2024-05-20 10:20:36] INFO: gtdbtk classify_wf --genome_dir /p300s/3-binning --out_dir /p300s/MAG/classify_wf --extension fa --cpus 1 --skip_ani_screen [2024-05-20 10:20:36] INFO: Using GTDB-Tk reference data version r214: /p300s/GTDB_software/release214 prodigal is not on the system path. [2024-05-20 10:20:36] ERROR: Controlled exit resulting from early termination.

[2] In addition, if I run a command on a server that can connect to the Internet and I get an error memory problem, how much memory is appropriate? $ ~/.conda/envs/gtdbtk-2.3.2/bin/gtdbtk classify_wf --genome_dir /p300s/3-binning --out_dir /p300s/MAG/classify_wf --extension fa --cpus 1 --skip_ani_screen ...... [2024-05-20 11:38:28] INFO: Aligning markers in 11 genomes with 1 CPUs. [2024-05-20 11:38:29] INFO: Processing 11 genomes identified as bacterial. Traceback (most recent call last): File "/home/zhaoxt/.conda/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/biolib_lite/seq_io.py", line 66, in read_fasta if not line.strip(): MemoryError

[Error] Failed to process sequence file: /p300s/GTDB_software/release214/msa/gtdb_r214_bac120.faa [2024-05-20 11:38:39] ERROR: Controlled exit resulting from early termination.

Looking forward to your reply.

zhaoxuetong commented 6 months ago

Sorry, I realized I didn't enter the virtual environment.